iGEMDOCK: a graphical environment of enhancing GEMDOCK using pharmacological interactions and post-screening analysis

Table 1 Pharmacological interactions and consensus interaction ratio on estrogen receptor α and thymidine kinase

Protein	Predicted pharmacological interactions	Consensus interaction ratio ^a	Related works
ERA	R394-H^b (0.80^c)	1.0	Form hydrogen bonding networks for ligand binding [26, 27]
	E353-H (0.64)	0.8
	H524-H (1.00)	1.0
	L387-V (1.00)	0.9	Form non-polar contacts with A-ring of sterols scaffolds [28, 29].
	L387-H (0.52)	0.2
	F404-V (0.90)	1.0
	V346-V (0.98)	0.5
	L391-V (0.61)	0.9
	L384-V (0.57)	0.9
	L525-H (0.53)	0.9
TK	R222-H (1.00)	0.8	Transfer phosphate in the substrate phosphorylation [30, 31, 36]
	R222-E (1.00)	0.0
	R222-V (0.62)	0.4
	R163-H (0.99)	0.6
	R163-E (0.40)	0.0
	R163-V (0.56)	0.8
	E83-V (0.54)	0.2
	Y101-H (0.40)	0.2	Form hydrogen bonds with thymidine; activity was decreased over 90% if Q125 mutated [32]
	Y101-V (0.45)	0.0
	Q125-H (0.40)	1.0
	Y172-V (1.00)	1.0	Sandwich the thymine moiety of substrates [33]
	M128-V (0.58)	1.0
	W88-V (0.87)	0.9	Constitute a pocket for ligand binding [33]
	H58-V (0.68)	0.9

^a The consensus interaction ratio of the residue i is defined as A_j/A, where A_j is the number of active compounds interacting to the residue i and A is total number of active compounds.
^b H, E and V are the interaction types.
^c The pharmacological preferences (i.e. W_j defined in Equation (1)).

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